/*
 * Copyright (c) 2016. Real Time Genomics Limited.
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

package com.rtg.reader;

import java.io.IOException;

import com.rtg.util.iterators.IteratorHelper;

import htsjdk.samtools.util.RuntimeIOException;

/**
 */
class FastqIterator extends IteratorHelper<FastqSequence> {
  private final SequenceDataSource mFastqReader;
  boolean mAtEnd = false;

  FastqIterator(SequenceDataSource fastqReader) {
    mFastqReader = fastqReader;
    step();
  }

  @Override
  protected final void step() {
    try {
      mAtEnd = !mFastqReader.nextSequence();
    } catch (IOException e) {
      throw new RuntimeIOException(e);
    }

  }

  @Override
  protected boolean atEnd() {
    return mAtEnd;
  }

  @Override
  protected FastqSequence current() {
    try {
      return new FastqSequence(mFastqReader.name(), mFastqReader.sequenceData(), mFastqReader.qualityData(), mFastqReader.currentLength());
    } catch (IOException e) {
      throw new RuntimeIOException(e);
    }
  }
}
